This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The LTQ-Velos ion trap is currently set to a default state of trapping 2000 ions during the MSn scans. Trapping more ions may improve our identifications since the LTQ-Velos is significantly faster than the original LTQ. We compare the number of peptides identified and spectra acquired between the different ion capacity experiments using C. elegans soluble lysate in both data-dependent acquisition and data-independent acquisition experiments.